This is a test @LilyAndres

This concentration points to CHEBI:15640 - 5-formyltetrahydrofolic acid, but it seems like the hasDbXrefs are coming in at too broad a level. Can the INFOODs and USDA_NDB tags be associated with concentrations at a more granular level? Is it really the case that multiple ones are correct for 5-formyltetrahydrofolic acid? Ideally INFOODs and USDA_NDB are only 1-1 DB Xrefs.

Following form the work in #52 we now have the issue that some classes are asserted as subclass to material entity when we only want them to show up in cdno-edit.owl as subclass to the appropriate terms from the dietary nutritional component hierarchy.

We'll need to remove the subclass axioms that are subclass to material entitiy, for example

For new term requests, please provide the following information:

Preferred term label

soluble dietary fibre

Textual definition

Water- soluble/well fermented fibres

Anita, FP. 1973.

Suggested parent term

dietary fibre

Preferred term label

resistant starch

Textual definition

Proceedings for the 2nd plenary meeting of EURESTA: European FLAIR Concerted Action

The total amount of starch, and the products of starch degradation that resists digestion in the small intestine of healthy people. The resistance of starch to digestion is influenced by the nature of the association between starch polymers, with higher amylose levels in the starch being associated with slower digestibility rates

Suggested parent term

soluble dietary fibre

Following an example such as https://github.com/FoodOntology/foodon/releases/tag/v0.4.8 follow the github release process and give a little description nothing to fancy just a small paragraph about CNDO and what it includes. ie. DNCs and chemical concentrations.

You can look at this envo release https://github.com/EnvironmentOntology/envo/releases/tag/v2020-06-10 for an example of how to name it. something like 2020-06-10 release

I need the CDN-DF v2.0 and the lookup table excel files to describe them in my thesis as supplementary data, therefore I would like to add them in the "utility" folder.

Following up on some discussion with @LilyAndres we have an opportunity for some potential interest and maybe adoption of CDNO by some of our collaborators. In our next release we'll need to make sure that we clarify that we've changed the axioms on original set of terms away form plant and to material to be more general. Normally this would merit deprecation and replacement, however, since our initial release 2021-02-08 was experimental and we did not yet have a user-base, we opted to simply change the axioms within the chemical concentration's while keeping the IDs the same. In our next release we'll need to make sure that's clear.

With @LilyAndres I will run the chemical_concentrations module.

CDNO is currently focused on 'concentration of' chemicals in 'plant structure'. The FoodOn ontology curation team is looking at concentrations of chemicals in animal and plant materials - including mercury in fish for example. One move would be to generalize all the CDNO concentration expressions to apply to 'organism' instead of just 'plant structure'? What are your thoughts on that?

Assuming CDNO could take on more general organism related concentrations, we'd then be in a position to contribute them. For example, there is a variation on your mercury concentration (probably not a subclass though) which is concentration of 'methylmercury compound' in organism, which I guess is the form commonly quantified in food.

We have a google sheet where we are working on the precomposed terms and patterns for high concentration of X in Y, and as well food classes having high (or low) concentrations.

Cheers,

Damion

In order to map the CDNO chemical concentration terms to existing labels or other information from the consortia such as the USDA or INFOODs, we'll need a new mapping robot template.

Preferred term label

plant secondary metabolite

Textual definition

A group of naturally occurring compound classes biosynthesized by differing biochemical pathways whose plant content and regulation is strongly susceptible to environmental influences and to potential herbal predators.

Pavarini D. et al., 2012

Suggested parent term

Parent CDNO 'dietary nutritional component'

Hi, I was wondering why capsaicin has for parent the lipid class ?

Suggested parent term

secondary plant metabolite

Attribution

https://orcid.org/0000-0001-6573-4070

Preferred term label

dietary nutritional component

Textual definition

An essential nutrient in food that is necessary to support human and livestock life for good health.

Suggested parent term

material entity - BFO:0000040

Preferred term label

Dry matter

Textual definition

Difference between the total weight and the moisture content.

doi.org/10.1046/j.0028-646X.2001.00320.x

Suggested parent term

Parent CDNO 'dietary nutritional component'

We'll make it be subclass to 'plant matter' [ENVO:01001121]. With an axiom linking to 'dry' [PATO:0001824]

I was expecting that when we ran make prepare release that it would call a robot reasoning routine on the cdno.owl file and have a clean concentration hierarchy, akin to running elk locally in the ontology. However, it did not. looking more into it other ontologies such as ENVO have the same workflow and don't seem to have ELK run to make a nicer hierarchy. There is probably a way to fix this using robot's reason command.

example of the concentration hierarchy when reasoned:

Vs the un-reasoned version we currently have in cdno.owl (after running make prepare release)

Preferred term label

trace element

Synonyms

micromineral

Textual definition

Minerals present in small quantities in humans and livestock which are also needed in small amounts in the diet

The University of Florida - EDIS

Suggested parent term

mineral nutrient - CHEBI:167164

As per ongoing discussions with @CropStoreDb @ramonawalls and @LilyAndres we will need to create terms for harvested materials which are the cross of NCBITaxon ids and PO plant parts. @LilyAndres has created a spreadsheet of relevant crops and their anatomical parts relevant to use-cases within the scope of CDNO here: CDNO_PO_harvested_materials. A preview of the sheet is as follows:

As we formulate an appropriate DOSDP or Robot Template, we'll want to capture the derives from relationship (or similar) between the PO and NCBITaxon terms respectively. These terms are intended to fill the part of some Y in the CDNO concentration of terms, of which the nutritional framework terms will inhere in.

concentration of and inheres in some (
    'Nutritional Framework Term' and
    part of some `Harvested Material Term`)

I wrote a python script to convert the NCF into the working Robot templates. I'll add that work to CDNO in a util directory in cdno/src/ontology.

Preferred term label

nutritional functional attribute

Textual definition

A functional attribute that inheres in one or more dietary nutritional component (or food material) and may contribute to a dietary role.

Suggested parent term

'specifically dependent continuant' [BFO:0000020]

Attribution

https://orcid.org/0000-0002-5975-6051

Import IAO so we can get IAO:0000115 showing up as definition/

Preferred term label

macromineral

Textual definition

Minerals present in large quantities in humans and livestock which are also needed in larger amounts in the diet.

The University of Florida - EDIS

Suggested parent term

mineral nutrient - CHEBI:167164

We'll leverage the ENVO chemical_concentration DOSDP for our new CDNO concentration terms. See ENVO's chemical_concentration.csv, and chemical_concentration.yaml.

We are going to create some nutritional framework terms in CDNO, the term is "free sugar" which does not exist in any other OBO ontology as far as I am aware

Preferred term label

free sugar

Textual definition

Based on Razlin's definition from Nutrition schema_framework_002:

Mono-, di-, or oligosaccharides that naturally occur freely, not bound or part of larger polysaccharides

Suggested parent term

digestible carbohydrate

For new term requests, please provide the following information:

Preferred term label

concentration of methylmercury compound in material entity

Synonyms

Textual definition

The concentration of methylmercury compound (http://purl.obolibrary.org/obo/CHEBI_25322) in some material entity.

Suggested parent term

concentration of trace element in material entity (http://purl.obolibrary.org/obo/CDNO_0200146)

(A FoodON nutritionist say this is the group of mercury compounds measured for mercury content in foodstuffs.
I think this is probably not a subclass of "concentration of mercury in plant structure". )

Attribution

https://orcid.org/0000-0002-8844-9165

We'll need to choose and add an appropriate license.

Here is the link with steps to integrate CDNO in OBO repository
We need to follow Step 3. Approval

We'll be making use of a Robot template to generate the Nutrition Schema Framework terms. As per FOODON's example, we'll use this google sheet to collaboratively edit the Robot template, and export it as a csv file and compile within the ontology.

Hey @LilyAndres, we'll need to add some descriptive information to our README.md. Definitely the title: Crop Dietary Nutrition Ontology, and any other supporting/descriptive information about the project. See ENVO's, or @ramonawalls BCO or PCO README.md files as examples.

Was there a technical/logic issue trying to position the hierarchy? I see:

This issue has been created to discuss the relationships of vitamins and their vitamers in CDNO and CHEBI.

1. We have ask CHEBI team, specially @amalik01 for clarification about the relationships described in CHEBI. One issue raised is the different relationships assigned to fat and water soluble vitamins. For example:

• The ‘B vitamin’ [CHEBI:75769] and ‘Vitamin C’ [CHEBI:21241] have the ‘is_a’ relationship with ‘water-soluble vitamin’ [CHEBI:27314].

• In contrast ‘Vitamin A’ [CHEBI:12777], ‘Vitamin D’ [CHEBI:27300], ‘vitamin E’ [CHEBI:33234] and ‘Vitamin K’ [CHEBI:28384] have the ‘has_role’ relationship with ‘fat-soluble vitamin’ [CHEBI:24020].

The term vitamer is not defined as such in CHEBI. However, some vitamer molecules have been assigned to specific vitamins with:

• ‘has_role’ = eg some vitamers from ‘B vitamin’ [CHEBI:75769] and ‘vitamin C’ [CHEBI:21241]

and the rest with

• ‘is_a’

See the following link:

The proposal from CHEBI is to

• assign 'is a' vitamin to both fat and water soluble vitamin

• assign the 'has role' relationship to all vitamers (in their case vitamin) molecules.

2. Within CDNO we propose to refine/extend the relationships, re-using where possible the CHEBI definitions.
Thus: (reading the relationships right to left)

3. We propose establishing definitions/relationships for vitamin roles within the ‘dietary_function’ class of CDNO.

A separate thread/issue will be generated to discuss this class.

What do you think?

Preferred term label

physical attribute

Textual definition

A physical property that inheres in a food material or one or more dietary nutritional component

Suggested parent term

'specifically dependent continuant' [BFO:0000020]

Attribution

https://orcid.org/0000-0002-5975-6051

This issue has been created to discuss the labels and reuse of CHEBI terms in the CDNO mineral nutrient class.

Having checked some CHEBI labels that were incorrectly re-labeled in CDNO (see issue #64), e.g. re-labeled as 'calcium', we identified some terms where the representation of mineral nutrients could be improved in the dietary nutrition domain:

1. We propose the reuse of other CHEBI terms. For example the ionic form (atom with more or less electrons) of an element is often measured when quantifying e.g. the 'concentration of calcium' in milk, typically using a method (eg ICP-MS) that estimates the concentration of calcium (2+) ions. However, the quantity being calculated is typically expressed as atomic Ca, even though it may be present in multiple bound, ionised or other molecular forms (eg salts). In some situations, there may be an assay that allows the estimation of concentration (via stoichiometry) of a specific salt.

Thus, within the 'dietary nutritional component' and 'dietary nutritional component concentration' classes, we would include eg. 'calcium(2+)' [CHEBI:29108] in addition to 'calcium atom' [CHEBI:22984].

2. To ensure there is vocabulary more tailored to dietary nutrition, we propose the adoption of the terms ‘dietary calcium’, ‘dietary magnesium’ etc, and under these have options for hierarchical sets of terms including: ‘calcium atom’, ‘calcium ion’, ‘calcium salt’.

We welcome feedback to know whether this provides a way forward to help nutritionists navigate to appropriate ChEBI terms and distinguish in what form an element may be present, quantified/estimated or reported depending on assay.

3. The hierarchical classification would look something like this, using 'calcium' as an example:

Preferred term label

dietary role

Textual definition

A biological role that may be assigned to a dietary nutritional component based on evidence that supports a function defined at the levels of molecular interaction, cellular process or physiological role.

Suggested parent term

'role' [BFO:0000023]

Attribution

https://orcid.org/0000-0002-5975-6051

Have been working various branchs/pseudo-branches to have a full solution to work from robot templates, merge in with CHEBI annotations, and import into cdno-edit.owl. Creating a branch to address this here.

We are going to create some nutritional framework terms in CDNO the term is "Water soluble protein" which does not exist in any other OBO ontology as far as I am aware

Preferred term label

Water soluble protein

Textual definition

Based on Razlin's definition from Nutrition schema_framework_002:

Major category of storage proteins that are soluble in proteins.

Suggested parent term

CHEBI:36080 - protein

Preferred term label

Free sugar

Textual definition

The World Health Organization defines free sugars as:

All monosaccharides and disaccharides which are part of foods or food additives.

Suggested parent term

Available carbohydrate in CDNO

As the coverage of CDNO is now "Compositional Dietary Nutrition Ontology" I would suggest to clarify the current hierarchy which is "dietary nutritional component"

Actually, they are a mismatch between compositional constituents and "real" nutritional components.

I mean we can enlarge the coverage of this branch by renaming it "compositional constituent" and then distinguish between nutrient subclasses and other subclasses (see my suggestion below)

This is the direction I am taking in my own work. I would be happy if we could agree on this.

We are going to create some nutritional framework terms in CDNO the first term is "Non digestible carbohydrate" which does not exist in any other OBO ontology as far as I am aware

Preferred term label

Non digestible carbohydrate

Textual definition

Based on Razlin's definition from Nutrition schema_framework_002:

Carbohydrate components which are not easily digestible, and form major part of dietary fibre (TDF)

Suggested parent term

CHEBI:16646 - carbohydrate

With @LilyAndres runing make prepare release to create all the files from the edit.

This was reported in a MAXO issue: monarch-initiative/MAxO#230 (comment)

Can you see if they are occurring as leftovers of a CHEBI import or artifacts of a chebi include file?

We are going to create some nutritional framework terms in CDNO the first term is "Digestible carbohydrate" which does not exist in any other OBO ontology as far as I am aware

Preferred term label

Digestible carbohydrate

Textual definition

Based on Razlin's definition from Nutrition schema_framework_002:

Also known as available carbohydrate corresponds to fractions of total carbohydrate that is digestible to provide energy.

Suggested parent term

CHEBI:16646 - carbohydrate

@LilyAndres noticed the following terms are miss-matched between the modules/mappings.owl and modules/chemical_concentration.owl files.

CDNO:0200181	5-formyltetrahydrofolic acid
CDNO:0200182	vitamin B

It should be an easy fix to just switch them in the templates/mappings.csv to be in the same order as they are in the templates/chemical_concentration.csv file.

Maybe @LilyAndres can double check to see if there are any others that got switched. I suspect this happened because there was some confusion about the vit b term, but so maybe its the only one but if were not sure it's good to check.

For new term requests, please provide the following information:

Preferred term label

Dietary fiber

Textual definition

Plant material that is resistant to enzymatic digestion.

PMID: 23729846

Suggested parent term

CHEBI:16646 - carbohydrate

Note about the definitions in the concentration terms, the grammer is a little off it's

The concentration of X when measured in plant structure.

It should be something like a plant structure. or some plant structure. @CropStoreDb and @LilyAndres any preferences? I think some works. I'll add this to the DOSDP file before we run all the new terms.

@LilyAndres what's the plan are you going to run the whole workflow soon? If so I we should quickly address this.

Preferred term label

insoluble dietary fibre

Textual definition

Water- insoluble/less fermented fibres

Suggested parent term

Antia, 1973

dietary fibre

Preferred term label

seed storage protein

Textual definition

A protein that accumulates in the developing seed with the intent to act as a storage reserve for nitrogen, carbon, and sulfur.

Suggested parent term

protein CHEBI:36080

I am in the process of deprecating FoodOn nutrient terms in favour of the CDNO ones. On the vitamin branch I've managed to eliminate FoodOn duplicates for the most part, but there are some vitamin B & C underlings that I'm not sure about. See the bolded FoodOn vitamin branch (which uses NCIT Vitamin term http://purl.obolibrary.org/obo/NCIT_C944) which will be obsoleted soon:

I wasn't sure if the underlings given on the FoodOn side should be added to the CHEBI side? Or are they erroneous?

We are going to create some nutritional framework terms in CDNO the term is "Salt soluble protein" which does not exist in any other OBO ontology as far as I am aware

Preferred term label

Salt soluble protein

Textual definition

Based on Razlin's definition from Nutrition schema_framework_002:

A family of globular proteins that have higher molecular weights than albumin, and makeup the majority of legume seed storage protein. Examples of globulin: legumin and vicillin (soybean). These proteins can cause allergic reactions if they bind with human IgE antibodies.

Suggested parent term

CHEBI:36080 - protein

@LilyAndres @CropStoreDb @ddooley @ramonawalls

Regarding the CDNO mappings, I realize it might not quite show up how you’d want/expect. In the robot template it makes sense as USDA and INFOODS are in the column headers.

However, those won’t get compiled so what will end up happening is we’ll get

Perhaps this is desired and we can stop there, however, if not I propose two possible solutions:

1. Change the annotation property from http://www.geneontology.org/formats/oboInOwl#hasDbXref to a newly invented one in CDNO perhaps something like http://www.geneontology.org/formats/oboInOwl#USDADbXref

2. Add something like USDA_ to the beginning of all the rows in the mappings csv and keep the hasDbXref annotation property.

That way it'll show up looking something like this:

I'd advocate for solution 2 but would like to hear everyone's thoughts/ suggestions.